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A protein is a biochemical, which along with carbohydrates, lipids, and nucleic acids make up a biological organism. Proteins are polymers of amino acids. There are over 20 different natural amino acids, and the sequence of them making up a given protein is determined by the genetic code held within DNA and its messenger copy RNA. Proteins which are capable of catalyzing a biochemical reaction are termed enzymes.
When folded into a three dimensional structure, the protein becomes a molecular machine. Some proteins are enzymes which help facilitate chemical reactions within a cell by reducing the energy requirements for those reactions. Other proteins are responsible for transporting chemicals in and out of cells, while others are structural parts of the cell. Examples of common proteins include actin and myosin are responsible for the mobility of muscle tissue; albumin which is involved in the regulation the balance of water and other chemicals in blood; and lipase which is the enzyme that breaks down lipids into their constituent fatty acid and glycerol molecules.
Proteins and enzymes are increasingly being used to replace traditional chemical synthesis because of the high specificity and selectivity they offer as well as reduced cost and lower amount of chemical waste. This is due to nature's billion year long evolution to find the most effective way of doing something.
A protein's structure is broken down into four parts.
- Primary structure: The sequence of amino acids that compose the protein.
- Secondary structure: Hydrogen bonding between certain amino acid residues cause the structure to twist into what is term the α-helix or β-sheet.
- Tertiary structure: The sequence then distorts into an overall structure.
- Quaternary structure: Several proteins can gather together to form a more active complex, such as haemoglobin, which is composed of four separate proteins attached together.
Once the amino acids are assembled into a chain, the chain folds, partially spontaneously and partially assisted by other proteins. In its folded state, it becomes active as either a form of transport through the cell wall or as an active enzyme.
The folding of proteins is often cited by Intelligent Design proponents as evidence of design and/or intervention by God. They will say that the folding is random and that the odds against a long protein folding into a specific conformation are astronomically huge, throwing in mind-boggling numbers or strange analogies about winning the lottery to confuse the situation. This would be true if the protein folding was random, which, of course, it isn't. Many properties of the amino acids used in the protein govern the folding. The hydrophobic (water hating) side chains of Leucine, for example, will fold inside the chain to get away from the water that is solvating the protein, while the hydrophilic (water loving) side chains of Lysine will move outward to meet the water. Another factor is that the proteins do not spontaneously fold, many are assisted by other proteins present in a cell. Thus, the process is governed by rules, not chance.
Amateur creationists (often with the aid of a flashy YouTube video) may also cry for the Second Law of Thermodynamics to come to their aid. As this law is often (mis)interpreted to mean that disorder can only increase with time, people without a sound knowledge of biology and chemistry may think that this prohibits a long, loose and disorganised peptide chain folding spontaneously to a tight, functioning and well-ordered protein. However, a long chain is solvated by many water molecules — often hundreds or thousands of H2O molecules surround the chain. On folding, these water molecules are released from their partial chemical bonds and overall disorder increases, despite the huge gain in order from the folding of the protein. The energetic release caused by the water is a thermodynamic driver for the formation of the folded and active protein. Besides, you aren't breaking the second law if there's a huge exterior source of energy driving evolution.